Question: Generate Heatmap after DEseq2 analysis
gravatar for nicolas.hipp
3.5 years ago by
Rennes, France
nicolas.hipp0 wrote:

Hi everyone,

I have a problem to represent my RNAseq data. I have a list of DE genes as output of DEseq2. So I would like to make an heatmap of these genes across all my conditions (3 conditions, and 3 samples per condition)

Problems starts here because I don't really know which values I have to take in input of DEseq2. Can I sort my DE gene-list and perform my heatmap with the values provided by the rlog function of DEseq2?

Sorry for the naive question, maybe i'm totally wrong. Thanks

rna-seq deseq2 • 2.1k views
ADD COMMENTlink modified 3.4 years ago by Nicolas Rosewick8.7k • written 3.5 years ago by nicolas.hipp0

Dear Nicolas, Hi

Please have a look at this Trinity page for "Automatically Partitioning Genes into Expression Clusters" and "Interactive analysis of DE features using MeV".

Maybe that could help.

~ Best

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Farbod3.3k

Hello :) Thanks for the answer, I will have a look on it. Best ;)

ADD REPLYlink written 3.4 years ago by nicolas.hipp0
gravatar for Nicolas Rosewick
3.4 years ago by
Belgium, Brussels
Nicolas Rosewick8.7k wrote:

Read the DESeq2 vignette. There is a section regarding heatmaps using transformed data vsd or rld

ADD COMMENTlink written 3.4 years ago by Nicolas Rosewick8.7k
gravatar for Ron
3.4 years ago by
United States
Ron990 wrote:

You can take the expression values (FPKMS )of those genes in the samples and plot a heat map.

ADD COMMENTlink written 3.4 years ago by Ron990
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